1 Biomark, Inc.

1 Introduction

The Bureau of Reclamation (BOR), Idaho Governor’s Office of Species Conservation (OSC), and an interdisciplinary team of partners have assembled an Upper Salmon Assessment Team to complete biologic and geomorphic analyses in support of future project identification, prioritization, and design in the Upper Salmon Subbasin, Idaho. The biologic and geomorphic analyses are being lead by Biomark Inc. (Biomark) and Rio Applied Science and Engineering (Rio ASE), respectively. Past efforts from the team resulted in the development of a watershed-scale Integrated Rehabilitation Assessment (IRA) in the Lemhi, Pahsimeroi, and Upper Salmon (Sawtooth Valley) watersheds. This initial phase of the project identified the “problem” by spatially quantifying capacity limitations for spring/summer Chinook salmon and summer run steelhead within a geomorphic context across these three watersheds. The second phase, termed the Multiple Reach Assessments (MRA), includes identifying appropriate and focused “solutions” to the identified capacity problems within four valley segments: Upper Lemhi, Lower Lemhi, Lower Pahsimeroi, and Upper Salmon (Decker Flats). To achieve this goal, the team will collaboratively summarize existing and targeted physical habitat conditions relative to documented habitat needs for specific species and life stages, including discussion of high-quality habitat, its creation, and its maintenance to inform future rehabilitation actions.

The goal of this document is to evaluate the hydraulic suitability of our four target valley segments under existing conditions to support select life stages of Chinook salmon and steelhead. This information can help identify geomorphic reaches where depth and velocity may be limiting to particular species and life stages which could prove useful for project prioritization.

1.1 Objective

Evaluate the composite suitability of geomorphic reaches in the upper Lemhi, lower Lemhi, lower Pahsimeroi, and upper Salmon (Decker Flat) valley segments based on modeled depth and velocity results available from Light Detection and Ranging (LiDAR) models available from those areas. Composite suitability is evaluated for both Chinook salmon and steelhead and for adult spawning and juvenile rearing at various discharge scenarios (see Table 2.1). We also provide the proportion of each geomorphic reach classified as simple, mixed, or complex for reference.

2 Methods

Composite suitability estimates were calculated as the geometric mean of depth and velocity suitability estimates.

2.1 Habitat Suitability

2.1.1 Chinook salmon

Figure 2.1 reference here

Suitability indices at varying depths and velocities for juvenile rearing and adult spawning for Chinook salmon from Maret et al. (2006).

Figure 2.1: Suitability indices at varying depths and velocities for juvenile rearing and adult spawning for Chinook salmon from Maret et al. (2006).

2.1.2 Steelhead

Figure 2.2 reference here

Suitability indices at varying depths and velocities for juvenile rearing and adult spawning for steelhead from Maret et al. (2006).

Figure 2.2: Suitability indices at varying depths and velocities for juvenile rearing and adult spawning for steelhead from Maret et al. (2006).

2.2 Scenarios

And finally, I’ll reference Table 2.1 here…

Table 2.1: Scenarios for which we evaluated the composite suitability (depth & velocity) within geomorphic reaches including the corresponding depth and velocity rasters used for each scenario.
Scenario Watershed Species Life Stage Season Depth Raster Velocity Raster
1 Lemhi Chinook Juvenile Summer D_Aug_All.tif V_Aug_All.tif
2 Lemhi Chinook Juvenile Winter d_jan_v2.tif v_jan_v2.tif
3 Lemhi Chinook Spawning Summer D_Aug_All.tif V_Aug_All.tif
4 Lemhi Steelhead Juvenile Summer D_Aug_All.tif V_Aug_All.tif
5 Lemhi Steelhead Juvenile Winter d_jan_v2.tif v_jan_v2.tif
6 Lemhi Steelhead Spawning Spring d_jan_v2.tif v_jan_v2.tif
7 Pahsimeroi Chinook Juvenile Summer - -
8 Pahsimeroi Chinook Juvenile Winter Pah_WLow_depth.tif Pah_WLow_velocity.tif
9 Pahsimeroi Chinook Juvenile Spring Pah_1pt5_depth.tif Pah_1pt5_velocity.tif
10 Pahsimeroi Chinook Spawning Summer Pah_WLow_depth.tif Pah_WLow_velocity.tif
11 Pahsimeroi Steelhead Juvenile Summer - -
12 Pahsimeroi Steelhead Juvenile Winter Pah_WLow_depth.tif Pah_WLow_velocity.tif
13 Pahsimeroi Steelhead Juvenile Spring Pah_1pt5_depth.tif Pah_1pt5_velocity.tif
14 Pahsimeroi Steelhead Spawning Spring Pah_1pt5_depth.tif Pah_1pt5_velocity.tif
15 Upper Salmon Chinook Juvenile Summer US_Summer75_depth.tif US_Summer75_velocity.tif
16 Upper Salmon Chinook Juvenile Winter US_Winter75_depth.tif US_Winter75_velocity.tif
17 Upper Salmon Chinook Juvenile Spring US_1pt5year_depth.tif US_1pt5year_velocity.tif
18 Upper Salmon Chinook Spawning Summer US_Summer75_depth.tif US_Summer75_velocity.tif
19 Upper Salmon Steelhead Juvenile Summer US_Summer75_depth.tif US_Summer75_velocity.tif
20 Upper Salmon Steelhead Juvenile Winter US_Winter75_depth.tif US_Winter75_velocity.tif
21 Upper Salmon Steelhead Juvenile Spring US_1pt5year_depth.tif US_1pt5year_velocity.tif
22 Upper Salmon Steelhead Spawning Spring US_1pt5year_depth.tif US_1pt5year_velocity.tif

3 Results

Results text here…

3.1 Upper Lemhi

Figure 3.1 reference here

Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Upper Lemhi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.1: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Upper Lemhi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.2 reference here

Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Upper Lemhi valley segment.

Figure 3.2: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Upper Lemhi valley segment.

3.2 Lower Lemhi

Figure 3.3 reference here

Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Lpper Lemhi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.3: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Lpper Lemhi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.4 reference here

Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Lower Lemhi valley segment.

Figure 3.4: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Lower Lemhi valley segment.

3.3 Pahsimeroi

Figure 3.5 reference here

Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Lower Pahsimeroi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.5: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Lower Pahsimeroi valley segment. Results for both Chinook salmon and steelhead and for three lifestages (adult spawning, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.6 reference here

Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Lower Pahsimeroi valley segment.

Figure 3.6: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Lower Pahsimeroi valley segment.

3.4 Upper Salmon

Figure 3.7 reference here

Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Upper Salmon (Decker Flat) valley segment. Results for both Chinook salmon and steelhead and for four lifestages (adult spawning, juvenile spring rearing, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.7: Violin plots showing the distribution of composite suitability values (geometric mean of depth and velocity suitability) across geomorphic reaches in the Upper Salmon (Decker Flat) valley segment. Results for both Chinook salmon and steelhead and for four lifestages (adult spawning, juvenile spring rearing, juvenile summer rearing, juvenile winter rearing) are shown. The bottom panel shows the proportion of each geometric reach classified as simple, mixed, or complex.

Figure 3.8 reference here

Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Upper Salmon (Decker Flat) valley segment.

Figure 3.8: Map showing the mean composite suitability by life stage and across geomorphic reaches for Chinook salmon and steelhead in the Upper Salmon (Decker Flat) valley segment.

4 Discussion

Some discussion crap here…

5 Literature Cited

Stuff we cite, but nobody ever actually read…